/*=========================================================================
 *
 *  Copyright SINAPSE: Scalable Informatics for Neuroscience, Processing and Software Engineering
 *            The University of Iowa
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
/*
 * Author: Hans J. Johnson
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * Redistributions of source code must retain the above copyright notice, this
 * list of conditions and the following disclaimer.
 *
 * Redistributions in binary form must reproduce the above copyright notice,
 * this list of conditions and the following disclaimer in the documentation
 * and/or other materials provided with the distribution.
 *
 * Neither the name of the Nathan Kline Institute nor the names of its
 * contributors may be used to endorse or promote products derived from this
 * software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 */

#include "itkIO.h"
#include <itkImageMomentsCalculator.h>
#include "TrimForegroundInDirection.h"
#include "itkLargestForegroundFilledMaskImageFilter.h"
#include <itkImageIteratorWithIndex.h>
#include <itkMinimumMaximumImageCalculator.h>
#include <itkHistogram.h>
#include <itkMath.h>
#include "itkFindCenterOfBrainFilter.h"

// #define USE_DEBUGGIN_IMAGES

SImageType::PointType
FindCenterOfBrainBasedOnTopOfHead(SImageType::Pointer & volOrig,
                                  unsigned int          axis,
                                  double                otsuPercentileThreshold,
                                  unsigned int          closingSize,
                                  double                headSizeLowerLimit,
                                  SImageType::PixelType BackgroundFillValue)
{
  SImageType::Pointer foreground = SImageType::New();

  return TrimForegroundInDirection(
    foreground, volOrig, axis, otsuPercentileThreshold, closingSize, headSizeLowerLimit, BackgroundFillValue);
}

// ////////////////////////////////////////////////////////////////////////
// ////////////////////////////////////////////////////////////////////////
SImageType::PointType
TrimForegroundInDirection(SImageType::Pointer & foreground,
                          SImageType::Pointer & volOrig,
                          unsigned int          axis,
                          double                otsuPercentileThreshold,
                          unsigned int          closingSize,
                          double                headSizeLowerLimit,
                          SImageType::PixelType BackgroundFillValue)
{
  using FindCenterFilter = itk::FindCenterOfBrainFilter<SImageType>;
  FindCenterFilter::Pointer findCenterFilter = FindCenterFilter::New();
  findCenterFilter->SetInput(volOrig);
  findCenterFilter->SetAxis(axis);
  findCenterFilter->SetOtsuPercentileThreshold(otsuPercentileThreshold);
  findCenterFilter->SetClosingSize(closingSize);
  findCenterFilter->SetHeadSizeLimit(headSizeLowerLimit);
  findCenterFilter->SetBackgroundValue(BackgroundFillValue);

  findCenterFilter->Update();

  foreground = findCenterFilter->GetModifiableTrimmedImage();
  SImageType::PointType center = findCenterFilter->GetCenterOfBrain();
  return center;
}
